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7/27/2019 Bc34lec3 Nucleic Acids
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Inhibitors of the Genetic
Mechanisms
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Macrolides
• Erythromycin is a naturally-occurring
macrolide derived from Streptomyces
erythreus
• Structural derivatives include clarithromycin and azithromycin:
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Macrolide Structure
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Macrolide binding in thecrytallographic structure of H.
marismortui 50S ribosomal subunit
http://www.ncbi.nlm.nih.gov/pubmed/11698379
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Aminoglycosides
• Initial discovery in the late 1940s, withstreptomycin being the first used; gentamicin,tobramycin and amikacin are most commonly usedaminoglycosides
• All derived from an actinomycete or aresemisynthetic derivatives
• Consist of 2 or more amino sugars linked to an
aminocyclitol ring by glycosidic bonds =aminoglycoside
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Aminoglycoside Structure
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AminoglycosidesMechanism of Action
• Multifactorial, but ultimately involvesinhibition of protein synthesis
• Irreversibly bind to 30S ribosomesdisrupting the initiation of proteinsynthesis, decreases overall proteinsynthesis, and produces misreading of
mRNA• Most are bacteriocidal
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Streptogramins
• Example: Synercid®
• synthetic pristinamycin derivatives in a
30:70 w/w ratio - Quinupristin:Dalfopristin
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Linezolid
Mechanism of Action
• Binds to the 50S ribosomal subunit near tosurface interface of 30S subunit – causes
inhibition of 70S initiation complex whichinhibits protein synthesis
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Clindamycin
Clindamycin is a semisynthetic derivative of
lincomycin which was isolated from
Streptomyces lincolnesis in 1962
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Clindamycin
Mechanism of Action
Ø Inhibits protein synthesis by binding
exclusively to the 50S ribosomal subunit
§ Binds in close proximity to macrolides –
competitive inhibition
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Tetracycline
• Tetracyclines inhibit
bacterial protein
synthesis by blocking
the attachment of thetransfer RNA-amino
acid to the ribosome.
More precisely they
are inhibitors of thecodon-anticodon
interaction.
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Metronidazole
Metronidazole is a synthetic nitroimidazole
antibiotic derived from azomycin. First found
to be active against protozoa, and then
against anaerobes where it is still extremelyuseful.
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Metronidazole
Mechanism of Action
Ø Ultimately inhibits DNA synthesis
§ Selective toxicity against anaerobic and
microaerophilic bacteria due to the presence of ferredoxins within these bacteria
§ Ferredoxins donate electrons to form highlyreactive nitro anion which damage bacterial
DNA and cause cell death
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Summary of antibiotic action on the
genetic mechanism
http://hstalks.com/main/view_talk.php?t=798&r=285&c=252
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Mutation and genetic
disorders
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Mutation
•
Hereditable change in DNA resulting from change innucleotide sequence
• Types of mutation – Point mutations
• Swap one base for another; insert a base; delete a base
– Macrolesions• Alteration of the number of copies of a short repeat and
• Large insertions into a gene
• Multiple causes – Spontaneous
• DNA replication/repair errors• Insertion of transposons
– Mutagens (physical, chemical, viral)
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DNA Mutations: An Overview
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Point Mutations• Single or few base pair changes
• Provide “background rate” of mutation – critically important to evolution
• More likely to lead to loss of function than gain of function
•
Causes point mutation – Induced• action of mutagen; environmental agent that alters nucleotide
sequence
• process of inducing mutations by mutagens called mutagenesis
– Spontaneous• arise in absence of known mutagen
• may be due to tautomerism
• may be caused by errors in DNA replication
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Types of point mutation
• Base substitution
– transition• A↔ G (purine↔ purine) (A·T↔ G·C)
• C↔ T (pyrimidine↔ pyrimidine) (C·G↔ T· A)
– transversion
• purine↔ pyrimidine (e.g., A↔ C) (A·T↔ C·G)
• Addition or deletion of nucleotide pairs (base-pair addition or deletion) – also called indel mutations
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Types of mutation and effects
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Functional consequences
• Missense mutations differ in severity – conservative AA substitution substitutes chemically
similar AA; less likely to alter function
– nonconservative AA substitution replaces chemically
different AA; more likely to alter function• Nonsense mutation results in premature termination
of translation
– truncated polypeptides often are nonfunctional
• Point mutation in non-coding region may or may not
have visible effect (e.g., regulatory region)
S t M t ti
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Spontaneous Mutation:
Tautomeric shift
• Natural variation in chemical form of base(isomers); differ in position of atoms & bonds – amino (normal)↔ imino (rare)
– keto (normal)↔ enol (rare)
• Results in mutation during DNA replication – base in rare tautomeric form pairs with chemically
similar base of its normal complement
– e.g., C·G↔ C*·G at replication results in C*· A whichresolves to C· A upon reverse of tautomeric shift
– at next DNA replication event, use of A strand resultsin T· A base pair, a transition
• Contributes to spontaneous mutation rate
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Common Tautomers & Base-
pairingThe more common ‘keto’ and ‘amino’ form of eachbase
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Rare tautomers
base-pair differentlythan the morecommon tautomers
T(enol) pairs with G
G(enol) pairs with T
C(imino) pairs with A
A(imino) pairs with C
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Tautomeric shifts can be a source of rare spontaneous mutation
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During the next round of DNA replication, the transitionmutation becomes “fixed” in the DNA.
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Creation of indel mutations
The slippage model for creation of insertions and deletions
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Induced mutation: Physical Agents
• Ultraviolet radiation – Thymine is most susceptible; UV radiation
generates thymine diradicals which can
dimerizes (pyrimidine-pyrimidine dimers) – activates SOS system, resulting in insertion of
incorrect base
• Ionizing radiation
– Generates free radicals from cleavage of molecules including H2O, bases, sugar-phosphate backbones
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Formation of the most toxic and mutagenic DNA lesion, cyclobutane-pyrimidine dimers by UV radiation.
Dimers can form between two adjacent pyrimidines. (A) thymine-thyminecyclobutane-pyrimidine dimer, and (B) thymine-cytosine dimer and their
photoreactivation by the enzyme photolyase in the presence of light.
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UV light inducesthe formation ofcyclobutane
dimers(pyrimidinedimers) and 6-4photoproducts
These products
cause significant‘kinks’ in theDNA and stopreplication andtranscription
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Free-radical effects
• Oxidative damage to bases
– caused by superoxide and peroxide radicals
– chemically alter base pairing properties
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Oxidatively Damaged Bases
Active oxygen species like superoxide radicals (O2), hydrogenperoxide (H2O2) and hydroxyl radicals (OH.) are produced byaerobic respiration and can damage DNA
Pairs with A
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Induced Mutation: Chemical agents
• Alkylating agents
• Intercalating agents
• Deaminating agents
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Alkylating Agents
• Depurination, spontaneous loss of G or A
• agent modifies base resulting in altered
pairing• e.g., EMS (ethyl methanesulfonate) and NG
(nitrosoguanidine), formaldehyde, CHCl3, epoxides
• results in replication block and insertion of nonspecific bases by SOS system
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Depurination occursmore often than youmight think
Mammalian cell losesabout 10,000 purinesfrom its DNA in a 20hour cell generationperiod
Obviously, theselesions must berepaired
Spontaneous Depurination
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Alkylating agent: substitutions
• Mutagens have different mutational
specificity
– Base analogs
• similar to nitrogenous bases of DNA, but havealtered pairing properties
• e.g., 5-bromouracil (5-BU) and 2-aminopurine (2-AP)
• result in transitions
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Action of 5-BU5-BU can frequently change to either the enol or ionized form
Causes G-C to A-T or A-T to G-C transitions
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Action of 2-APSimilar to 5-BU but with a different specificity
A-T to G-C transitions and G-C to A-T transitions
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Intercalating agents
• flat, planar molecules intercalate between
base pairs, disrupt DNA synthesis
– e.g., proflavin, acridine orange, aflatoxin,
benzo(a)pyrene
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Intercalating agentscan cause single baseadditions and deletions
R ti I t l ti
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Reactive Intercalation:
Aflatoxin
Aflatoxin modifies guanine andresults in loss of base in DNA
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Deamination
• Deamination, converts cytosine to uracil
which pairs with adenine at replication
• Indel mutations
– result in translation frameshift
– often occur in regions of repeated bases
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Deamination of C yields U whichbase pairs with A
Results in C-G toT-A transition
This occurs
spontaneously
Deamination
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Hotspots for mutation often reflect an aspect of the DNAsequence, for example, a sequence repeat
FS5, FS25, FS45, FS65 result from addition of one set of CTGG which isrepeated three times in the lacI gene
FS2, FS84 result from loss of one set of CTGG
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The Ames test was developedby Bruce Ames for evaluatingvarious chemicals for theirpotential as mutagens andcarcinogens
The Ames Test
1. Chemical injected into
mouse where it is metabolized
2. Liver (site of most chemicalmetabolism) is isolated and anextract is made that containsthe metabolized chemical
3. Extract is tested for mutagenicityin 3 strains of Salmonella to score forvarious kinds of mutations
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Defense mechanisms
• Free radical scavengers
– Vitamins A, E, C; only C is water soluble and
does not accumulate in the body
– GSH (glutathione) converted to GSSG
– Metallothionein (61 amino acids with 20
cysteines and 7 zinc atoms
• Enzymes – Photolyase: photoreactivation repair
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Photoreactivation repair
• Various enzymes with specific properties,
e.g. cleavage of pyrimidine dimers (T^T)
– enzyme binds to dimer
– energy of blue light cleaves bond
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Defense mechanisms: enzymes
– Demethylase (suicide enzyme)
– Superoxide dismutase (converts superoxides
to H2O2)
– Catalase (converts H2O2 to H2O + O2
– Peroxidases
• Repair systems
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Defense mechanisms: DNA Repair
• DNA damage must be repaired
• Damaged DNA in any cell will be deleterious to
cellular function
– in germ line cells mutations heritableBacteria are particularly prone to damage
– haploid all mutations are dominant
– unicellular whole organism affected
• Repair most effective before replication at site
• Repair can be more or less error-prone
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Types of Repair: Mismatch
• Mismatch repair genes: mut
• Mismatched bp detected
• Nearby ss cut and excision of ssDNA
past mismatch
• – daughter strand preferentially excised
• DNA polymerase repairs gap
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Apurinic gap repair
• Apurinic gaps
– most common spontaneous degradation of
DNA
– hydrolysis of sugar-purine bond - loss of purine(A, G)
• Repair by AP endonuclease
– removes base, ss gap filled by polymerase• If no repair then A inserted at replication
– G-C → T-A transversion mutation
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Excision repair
• Multi-enzyme system
• Repairs stretch of damaged nt’s
– damaged ssDNA excised
– gap repair by polymerase
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Nucleotide-excision
repair removes bulky
DNA lesions that
distort the doublehelix
http://www.nature.com/
scitable/resource?action=showFullImageF
orTopic&imgSrc=36086/pierce-17_30_FULL.jpg
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Post-replication repair
• Polymerase can’t replicate acrossdamaged nt’s
• Leaves a ss gap
• Gap filled by strand exchange from theother dsDNA
• Secondary gap repaired by polymerase